Character mistake: Hodgins is talking to Bones and says something about Goodman not being able to see his family and Zach not being able to see his kids. Goodman has kids, Zach was going to visit his family, not the other way around.
Character mistake: When Booth is locked in the ship, his "hallucination" asks Booth why he never bothered to learn some lock picking skills. However, in the episode "Judas on a Pole," Bones tells Booth that she's been practicing some lock picking skills that Booth taught her.
Character mistake: The finger bone found in the dead man's hand was said to come from somewhere near Assateague Island, to which Hodgins replies, "That's where the money pit is." The "Money Pit" is actually located on Oak Island in Nova Scotia, not on Assateague Island, in Maryland/Virginia. He also says that they dug it out to about 150 feet, which is also incorrect. The 1971 Triton excavation was able to dig a shaft to a depth of 235 feet. What is said to be on Assateague island is the legendary lost Spanish galleon La Galga, not the Money Pit. (00:02:55)
Character mistake: Hodgins discovers sap from a Japanese cherry tree on the bone from the nest. When the new graduate assistant suggests that it is one of the cherry trees at the Jefferson Memorial, Hodgins is skeptical of the information. In reality everyone who has lived in DC knows about the Japanese cherry trees at the memorial. They have an entire festival attributed to it every year and it practically shuts down the city with tourists. Hodgins should have known about the trees to begin with. (00:01:45)
Character mistake: While visiting Hanover Prep, Booth asks what "Omnia Mea Mecum Porto" meant, insinuating that he didn't know Latin. However, in later episodes every time he translates Latin he brings up that he was an altar boy, therefore he should have known Latin during this episode. (03:41:00)
Character mistake: Hodgins flies a decapitated human head via drone all the way from the crime scene to the Jeffersonian. A distance of several miles over city and urban landscapes. This would comprise all the evidence and be a massive risk to public health. Dr. Hodgins would know how much it would mess up the evidence since his area of expertise is particulates, and insects, both of which would be compromised. (00:28:30)
Character mistake: When Bones and Dr Hodgins, who is proclaimed as a seasoned diver in a previous episode, are in the tank, Bones gives an instruction and Hodgins replies with a thumbs up. Since Bones is diving as well, they both would know from certification (without which neither would be allowed to dive in the facility) classes that a thumbs up is the hand signal for "I'm ascending", not OK or any form of acknowledgement. They either are not certified divers or they should have immediately surfaced. (00:06:30)
Character mistake: When Booth mentions the 2007 Led Zeppelin concert in London, he comments that they toured that year. That Zeppelin concert was not part of a tour, but just a one-off reunion to honor the memory of late Atlantic Records executive Ahmet Ertegun.
Character mistake: Zach, from his hospital bed, says he used 3 grams of the monomer to make the explosion. 3 grams of a powder would be a very small amount; less than a teaspoonful. But when he actually did use it, he took a loose amount in a large tablespoon. Zach would have carefully measured it in order to be precise; but he did not. So this is a factual error in what he says; it is also a character mistake in that Zach is the personification of technical accuracy, and would never take a casual spoonful - especially of an explosive.
Character mistake: In season 2, episode 4, when they find the girl buried under the cross, you can see her face, which means she was on her back, because her neck couldn't possibly bend that far around without it being noted by Dr. Brennan later in the episode (which it isn't). Later in the episode, however, Special Agent Booth tells Epps' wife that she was found buried face down. (00:14:15 - 00:17:30)